5-35952038-C-T

Position:

• chr5-35952038-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152404.4(UGT3A1):​c.*2164G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,988 control chromosomes in the GnomAD database, including 4,046 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.21 (4046 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UGT3A1 NM_152404.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471

Genes affected

UGT3A1 (HGNC:26625): (UDP glycosyltransferase family 3 member A1) Enables glucuronosyltransferase activity. Part of UDP-N-acetylglucosamine transferase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGT3A1	NM_152404.4	c.*2164G>A		3_prime_UTR_variant	7/7	ENST00000274278.8	NP_689617.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT3A1	ENST00000274278	c.*2164G>A		3_prime_UTR_variant	7/7	1	NM_152404.4	ENSP00000274278.3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32109 AN: 151868 Hom.: 4049 Cov.: 32

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.208

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.211 AC: 32105 AN: 151988 Hom.: 4046 Cov.: 32 AF XY: 0.213 AC XY: 15835 AN XY: 74266

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.0854

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.210

Alfa AF: 0.238 Hom.: 2206

Bravo AF: 0.195

Asia WGS AF: 0.187 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1993879; hg19: chr5-35952140;